virtual tribool less(const Spectrum& lhs,
const Spectrum& rhs) const
{
CVParam lhsMSLevel = lhs.cvParam(MS_ms_level);
CVParam rhsMSLevel = rhs.cvParam(MS_ms_level);
if (lhsMSLevel.empty() || rhsMSLevel.empty())
return boost::logic::indeterminate;
return lhsMSLevel.valueAs<int>() < rhsMSLevel.valueAs<int>();
}
PWIZ_API_DECL string LegacyAdapter_Software::name() const
{
CVParam softwareParam = impl_->software->cvParamChild(MS_software);
if (softwareParam.cvid != CVID_Unknown)
return softwareParam.name();
string result = getProcessingMethodUserParamValue("name", impl_->software, impl_->msd);
return !result.empty() ? result : "unknown software name";
}
string LegacyAdapter_Instrument::Impl::get(const ParamContainer& paramContainer, CVID cvid, const string& userParamName)
{
// cvParam
CVParam param = paramContainer.cvParamChild(cvid);
if (param.cvid != CVID_Unknown)
return param.name();
// userParam
string result = paramContainer.userParam(userParamName).value;
if (result.empty()) result = "Unknown";
return result;
}
void writeSpectrumText(SpectrumPtr s, ostream& os)
{
os << std::setprecision(7); // 124.4567
// Write the scan numbers
os << "S\t";
int scanNum = getScanNumber(s);
os << scanNum << "\t" << scanNum << "\t";
// Write the precursor mz
Precursor& precur = s->precursors[0];
SelectedIon& si = precur.selectedIons[0];
double mz = si.cvParam(MS_selected_ion_m_z).valueAs<double>();
os << mz << "\n";
// Write the scan time, if available
if( s->scanList.scans[0].cvParam(MS_scan_start_time).timeInSeconds() )
os << "I\tRTime\t" << s->scanList.scans[0].cvParam(MS_scan_start_time).timeInSeconds() << "\n";
// Collect charge and mass info
vector<int> charges;
vector<double> masses;
int numChargeStates = 0;
// for each selected ion
BOOST_FOREACH(const SelectedIon& curIon, precur.selectedIons){
numChargeStates += getChargeStates(curIon, charges, masses);
}
// Write EZ lines if accurate masses are available
CVParam massParam = si.cvParam(MS_accurate_mass);
if( !massParam.empty() ){
for(int i=0; i < numChargeStates; i++){
os << "I\tEZ\t" << charges[i] << "\t" << masses[i] << "\t0\t0" << endl; // pad last two fields with 0
}
}
// For each charge, write the charge and mass
for(int i = 0; i < numChargeStates; i++)
{
os << "Z\t" << charges[i] << "\t" << masses[i] << "\n";
}
// Write each mz, intensity pair
const BinaryDataArray& mzArray = *s->getMZArray();
const BinaryDataArray& intensityArray = *s->getIntensityArray();
for (size_t p=0; p < s->defaultArrayLength; ++p)
{
os << mzArray.data[p] << " " << intensityArray.data[p] << "\n";
}
}
void writeSpectrumBinary(SpectrumPtr s, int version, bool compress, ostream& os)
{
// todo
// MSnScanInfo header(s);
// header.writeSpectrumHeader(version, compress, os);
int scanNum = getScanNumber(s);
os.write(reinterpret_cast<char *>(&scanNum), sizeIntMSn);
os.write(reinterpret_cast<char *>(&scanNum), sizeIntMSn); // Yes, there are two
Precursor& precur = s->precursors[0];
SelectedIon& si = precur.selectedIons[0];
double mz = si.cvParam(MS_selected_ion_m_z).valueAs<double>();
os.write(reinterpret_cast<char *>(&mz), sizeDoubleMSn);
float rt = (float) s->scanList.scans[0].cvParam(MS_scan_start_time).timeInSeconds();
os.write(reinterpret_cast<char *>(&rt), sizeFloatMSn);
if (version >= 2)
{
float basePeakIntensity = s->cvParam(MS_base_peak_intensity).valueAs<float>();
os.write(reinterpret_cast<char *>(&basePeakIntensity), sizeFloatMSn);
double basePeakMZ = s->cvParam(MS_base_peak_m_z).valueAs<double>();
os.write(reinterpret_cast<char *>(&basePeakMZ), sizeDoubleMSn);
// We don't have this information, but we need to write something,
// so pad with 0's. (version 2 specific data)
double conversionFactorA = (double)0;
os.write(reinterpret_cast<char *>(&conversionFactorA), sizeDoubleMSn);
double conversionFactorB = (double)0;
os.write(reinterpret_cast<char *>(&conversionFactorB), sizeDoubleMSn);
double tic = s->cvParam(MS_total_ion_current).valueAs<double>();
os.write(reinterpret_cast<char *>(&tic), sizeDoubleMSn);
// TODO
float ionInjectionTime = (float)0;
os.write(reinterpret_cast<char *>(&ionInjectionTime), sizeFloatMSn);
}
vector<int> charges;
vector<double> masses;
int numChargeStates = 0;
BOOST_FOREACH(const SelectedIon& curIon, precur.selectedIons)
{
numChargeStates += getChargeStates(curIon, charges, masses);
}
os.write(reinterpret_cast<char *>(&numChargeStates), sizeIntMSn);
bool hasAccurateMass = false;
if (version == 3)
{
int numEzStates = 0;
CVParam massParam = si.cvParam(MS_accurate_mass);
if (!massParam.empty())
{
numEzStates = numChargeStates;
hasAccurateMass = true;
}
os.write(reinterpret_cast<char *>(&numEzStates), sizeIntMSn);
}
int numPeaks = (int) s->defaultArrayLength;
os.write(reinterpret_cast<char *>(&numPeaks), sizeIntMSn);
// end spectrum header info
// Write out each charge state and corresponding mass
for(int i = 0; i < numChargeStates; i++)
{
os.write(reinterpret_cast<char *>(&(charges[i])), sizeIntMSn);
os.write(reinterpret_cast<char *>(&(masses[i])), sizeDoubleMSn);
}
// if there are accurate masses, write out EZ entries
if( hasAccurateMass ){
float blank = 0; // we don't have rTime or area, pad with zeros
for(int i=0; i < numChargeStates; i++){
os.write(reinterpret_cast<char *>(&charges[i]), sizeIntMSn);
os.write(reinterpret_cast<char *>(&masses[i]), sizeDoubleMSn);
os.write(reinterpret_cast<char *>(&blank), sizeFloatMSn);
os.write(reinterpret_cast<char *>(&blank), sizeFloatMSn);
}
}
// Do we need to write compressed m/z, intensity arrays?
if (compress)
{
writeCompressedPeaks(s, os);
}
else
{
// No need to compress, just write out the arrays
const BinaryDataArray& mzArray = *s->getMZArray();
const BinaryDataArray& intensityArray = *s->getIntensityArray();
for(int i = 0; i < numPeaks; i++)
{
double mzPeak = mzArray.data[i];
os.write(reinterpret_cast<char *>(&mzPeak), sizeDoubleMSn);
float intensityPeak = (float) intensityArray.data[i];
os.write(reinterpret_cast<char *>(&intensityPeak), sizeFloatMSn);
}
}
}
void writeSpectrumText(SpectrumPtr s, ostream& os)
{
os << std::setprecision(7); // 123.4567
bool ms1File = s->cvParam(MS_ms_level).valueAs<int>() == 1;
// Write the scan numbers
os << "S\t";
int scanNum = getScanNumber(s);
os << scanNum << "\t" << scanNum;
if (!ms1File)
{
// Write the precursor mz
Precursor& precur = s->precursors[0];
double mz = precur.isolationWindow.cvParam(MS_isolation_window_target_m_z).valueAs<double>();
os << "\t" << mz;
}
os << "\n";
// Write the scan time, if available
if( !(s->scanList.empty()) && s->scanList.scans[0].cvParam(MS_scan_start_time).timeInSeconds() )
os << "I\tRTime\t" << s->scanList.scans[0].cvParam(MS_scan_start_time).timeInSeconds()/60 << "\n";
if (s->defaultArrayLength > 0)
{
// Write the base peak intensity and base peak m/z
if (s->hasCVParam(MS_base_peak_intensity))
{
double bpi = s->cvParam(MS_base_peak_intensity).valueAs<double>();
os << "I\tBPI\t" << bpi << "\n";
}
if (s->hasCVParam(MS_base_peak_m_z))
{
double bpm = s->cvParam(MS_base_peak_m_z).valueAs<double>();
os << "I\tBPM\t" << bpm << "\n";
}
// Write the total ion current
if (s->hasCVParam(MS_total_ion_current))
{
double tic = s->cvParam(MS_total_ion_current).valueAs<double>();
os << "I\tTIC\t" << tic << "\n";
}
}
//TODO
// Write ConvA/ConvB information
// Write the ion injection time
//os << "I\tIIT\t" << s->scanList.scans[0].cvParam(MS_ion_injection_time).timeInSeconds()/60 << "\n";
if (!ms1File)
{
Precursor& precur = s->precursors[0];
SelectedIon& si = precur.selectedIons[0];
// Collect charge and mass info
vector<int> charges;
vector<double> masses;
int numChargeStates = 0;
// for each selected ion
BOOST_FOREACH(const SelectedIon& curIon, precur.selectedIons){
numChargeStates += getChargeStates(curIon, charges, masses);
}
// Write EZ lines if accurate masses are available
CVParam massParam = si.cvParam(MS_accurate_mass_OBSOLETE);
if( !massParam.empty() ){
for(int i=0; i < numChargeStates; i++){
os << "I\tEZ\t" << charges[i] << "\t" << masses[i] << "\t0\t0" << endl; // pad last two fields with 0
}
}
// For each charge, write the charge and mass
for(int i = 0; i < numChargeStates; i++)
{
os << "Z\t" << charges[i] << "\t" << masses[i] << "\n";
}
}
